1 Setup

source("helper_functions.R")
library(cytokit)
library(ggedit)
library(kableExtra)
library(monocle)
library(patchwork)
library(readxl)
library(readr)
library(R.utils)
library(Seurat)
library(tidyverse)
library(viridis)
sample <- c("joint_pons.seurat")
tables_directory <- "tables"
dir.create(tables_directory, showWarnings = FALSE)
monocle_objects_directory <- "monocle_objects"
dir.create(monocle_objects_directory, showWarnings = FALSE)

1.1 Load Seurat objects

input_directory <- "/mnt/KLEINMAN_SCRATCH/projects/sjessa/from_hydra/single_cell/2019-02_revision1/output/atlas-02"
load(file.path(input_directory, "joint_pons.seurat.Rda"))
seurat <- joint_pons
#For some reasons, there is now seurat@misc$colours and seurat@misc$colours_orig
seurat@misc$colours <- seurat@misc$colours_orig

1.2 Convert Seurat object to Monocle object.

# Convert cluster numbers to format used in levels(seurat@ident)
selected_clusters <- c(20, 13, 15, 3, 6, 11)
selected_clusters <- paste0("^", selected_clusters, "-")
selected_clusters <- grep(paste(selected_clusters,collapse="|"), levels(seurat@ident), value=TRUE)

# Colour vector is not available in this object for these cluster IDs, so they must be recovered a saved object. seurat@misc$colours and seurat@misc$colours_orig are identical vectors. Bug will be fixed later, according to Selin.
# First, recover corresponding new cluster ID.
load("/mnt/KLEINMAN_SCRATCH/projects/sjessa/from_hydra/single_cell/2019-02_revision1/output/atlas-02/palettes_joint.Rda")
seurat@misc$colours <- pal_jp
# Cluster columns also need to be renamed.
seurat@meta.data$cluster <- as.character(seurat@meta.data$cluster_joint)

monocle <- seurat_to_monocle(seurat, selected_clusters)
#monocle <- orderCells(monocle, reverse=TRUE)
colours <- monocle@experimentData@other$colours

2 Monocle plots

2.1 Cell trajectories

p <- plot_cell_trajectory(monocle, color_by="cluster", show_branch_points=FALSE) + scale_color_manual(values=colours)
p <- p + theme(legend.title=element_blank())
show(p)

p <- p + facet_wrap(~cluster) + theme(legend.position = "none")
show(p)

plot_cell_trajectory(monocle, color_by="Pseudotime", show_branch_points = TRUE)

plot_cell_trajectory(monocle, color_by="State", show_branch_points=TRUE)

p <- plot_complex_cell_trajectory(monocle, color_by="cluster", show_branch_points=FALSE) + scale_color_manual(values=colours)
p <- p + theme(legend.title=element_blank())
show(p)

2.2 Differentially expressed genes across pseudotime

2.2.1 All genes

diff_test_res_all_genes <- differentialGeneTest(monocle,
      fullModelFormulaStr = "~sm.ns(Pseudotime)", cores=12)
sig_gene_names_all_genes <- row.names(subset(diff_test_res_all_genes, qval < 0.1))
plot_pseudotime_heatmap(monocle[sig_gene_names_all_genes,],
      cores = 12,
      num_clusters=1,
      show_rownames = FALSE)

diff_test_res_all_genes <- diff_test_res_all_genes %>% rownames_to_column("gene")
write.table(diff_test_res_all_genes, file.path(tables_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11_diff_test_res_all_genes.txt"), sep="\t", quote=FALSE, row.names = FALSE)

2.2.2 Transcription factors

input_directory <- "/mnt/KLEINMAN_SCRATCH/projects/blancha/analyses/njabado/single_cell/annotation/animaltfdb3.0"
input_file <- "Mus_musculus_TF.txt"
transcription_factors <- read_tsv(file.path(input_directory, input_file), col_types = cols())

2.2.2.1 Pseudotime heatmaps of significant transcription factors

2.2.2.1.1 q value < 5*10^-5
significant_genes_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, qval < 5*10^-5) %>% .$gene 
cat("Number of significant genes: ", length(significant_genes_q_value_5_10_minus_5))
## Number of significant genes:  4944
significant_transcription_factors_q_value_5_10_minus_5 <- as.character(significant_genes_q_value_5_10_minus_5[significant_genes_q_value_5_10_minus_5 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_5_10_minus_5))
## Number of significant transcription factors: 311
plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=3, return_heatmap=TRUE, show_rownames = TRUE)

plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)

# The RMarkdown PDF has issues, hence this custom function to save the PDF file.
save_pheatmap_pdf(plot_genes_heatmap_output_q_value_5_10_minus_5[[2]], file.path("figures", "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11", "diff_test_res_plots_transcription_factors_only_q_value_5_10_minus_5_heatmap_custom.pdf"), width=16, height=36)
## pdf 
##   2
heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
ph_res_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[2]]
pheatmap_ordering_q_value_5_10_minus_5 <- rownames(heatmap_matrix_q_value_5_10_minus_5[ph_res_q_value_5_10_minus_5$tree_row[["order"]],])

transcription_factors_table_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_5_10_minus_5)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_5_10_minus_5 <- transcription_factors_table_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))

write.table(transcription_factors_table_q_value_5_10_minus_5, file.path(tables_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5.txt"), sep="\t", quote=FALSE, row.names=FALSE)

heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
heatmap_matrix_q_value_5_10_minus_5 <- as.data.frame(heatmap_matrix_q_value_5_10_minus_5) %>% rownames_to_column("gene")
heatmap_matrix_q_value_5_10_minus_5 <- heatmap_matrix_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
heatmap_matrix_q_value_5_10_minus_5 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")
gene 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
Id3 -1.1437784 -1.0989690 -1.0540253 -1.0089629 -0.9637975 -0.9185447 -0.8732207 -0.8278417 -0.7824240 -0.7369842 -0.6915390 -0.6461053 -0.6007001 -0.5553406 -0.5100441 -0.4648281 -0.4197103 -0.3747084 -0.3298402 -0.2851239 -0.2405774 -0.1962192 -0.1520675 -0.1081409 -0.0644578 -0.0210370 0.0221028 0.0649427 0.1074638 0.1496471 0.1914735 0.2329238 0.2739790 0.3146196 0.3548263 0.3945799 0.4338609 0.4726498 0.5109271 0.5486734 0.5858691 0.6224947 0.6585306 0.6939572 0.7287549 0.7629042 0.7963854 0.8291790 0.8612655 0.8926253 0.9232331 0.9529433 0.9814938 1.0086167 1.0340435 1.0575046 1.0787301 1.0974497 1.1133930 1.1262901 1.1358713 1.1418682 1.1440132 1.1420408 1.1356873 1.1246917 1.1087961 1.0877460 1.0612913 1.0291869 0.9911929 0.9470761 0.8966104 0.8395778 0.7757695 0.7049871 0.6270437 0.5417652 0.4489923 0.3485815 0.2404074 0.1243647 0.0003702 -0.1316346 -0.2716806 -0.4197687 -0.5758662 -0.7398891 -0.9112727 -1.0889214 -1.2717184 -1.4585612 -1.6483677 -1.8400814 -2.0326782 -2.2251720 -2.4166207 -2.6061315 -2.7928663 -2.9760462
Zfp706 -0.0765897 -0.0367229 0.0031568 0.0429950 0.0827369 0.1223276 0.1617117 0.2008333 0.2396363 0.2780644 0.3160609 0.3535686 0.3905303 0.4268884 0.4625849 0.4975617 0.5317605 0.5651226 0.5975893 0.6291017 0.6596006 0.6890267 0.7173207 0.7444232 0.7702746 0.7948153 0.8179860 0.8397269 0.8599787 0.8786819 0.8957773 0.9112057 0.9249083 0.9368263 0.9469012 0.9550749 0.9612896 0.9654879 0.9676127 0.9676074 0.9654160 0.9609831 0.9542536 0.9451735 0.9336891 0.9197476 0.9032970 0.8842863 0.8626651 0.8383843 0.8113982 0.7817161 0.7494001 0.7145148 0.6771253 0.6372972 0.5950965 0.5505898 0.5038436 0.4549249 0.4039011 0.3508394 0.2958074 0.2388727 0.1801030 0.1195658 0.0573289 -0.0065404 -0.0719745 -0.1389063 -0.2072688 -0.2769951 -0.3480188 -0.4202737 -0.4936939 -0.5682139 -0.6437688 -0.7202938 -0.7977250 -0.8759986 -0.9550516 -1.0348215 -1.1152463 -1.1962648 -1.2778162 -1.3598406 -1.4422786 -1.5250717 -1.6081603 -1.6914843 -1.7749841 -1.8586009 -1.9422770 -2.0259553 -2.1095796 -2.1930948 -2.2764465 -2.3595812 -2.4424465 -2.5249907
Id1 1.4871422 1.4381725 1.3894833 1.3411226 1.2931377 1.2455749 1.1984795 1.1518958 1.1058674 1.0604368 1.0156456 0.9715347 0.9281439 0.8855122 0.8436780 0.8026786 0.7625507 0.7233304 0.6850529 0.6477527 0.6114640 0.5762202 0.5420543 0.5089987 0.4770855 0.4463464 0.4168129 0.3885160 0.3614870 0.3357566 0.3113557 0.2883152 0.2666661 0.2464396 0.2276672 0.2103805 0.1946119 0.1803940 0.1677600 0.1567441 0.1473808 0.1397059 0.1337558 0.1295683 0.1271821 0.1266372 0.1279752 0.1312388 0.1364727 0.1437230 0.1530277 0.1642137 0.1769041 0.1907122 0.2052487 0.2201220 0.2349368 0.2492952 0.2627959 0.2750354 0.2856078 0.2941061 0.3001230 0.3032521 0.3030896 0.2992353 0.2912950 0.2788825 0.2616214 0.2391483 0.2111148 0.1771908 0.1370677 0.0904614 0.0371163 -0.0231912 -0.0906488 -0.1654039 -0.2475593 -0.3371692 -0.4342341 -0.5386972 -0.6504391 -0.7692745 -0.8949478 -1.0271304 -1.1654176 -1.3093116 -1.4577780 -1.6092531 -1.7622270 -1.9152926 -2.0671595 -2.2166656 -2.3627842 -2.5046291 -2.6414553 -2.7726568 -2.8977616 -3.0000000
Msx2 1.2595102 1.2236724 1.1881777 1.1530591 1.1183487 1.0840771 1.0502741 1.0169680 0.9841864 0.9519556 0.9203010 0.8892473 0.8588179 0.8290356 0.7999225 0.7714997 0.7437877 0.7168065 0.6905755 0.6651133 0.6404384 0.6165687 0.5935217 0.5713147 0.5499647 0.5294887 0.5099033 0.4912253 0.4734715 0.4566586 0.4408036 0.4259237 0.4120364 0.3991596 0.3873115 0.3765109 0.3667772 0.3581305 0.3505915 0.3441820 0.3389245 0.3348426 0.3319609 0.3303056 0.3299037 0.3307839 0.3329766 0.3365135 0.3414283 0.3477566 0.3555239 0.3644971 0.3741921 0.3841093 0.3937433 0.4025829 0.4101117 0.4158099 0.4191568 0.4196341 0.4167297 0.4099428 0.3987892 0.3828077 0.3615669 0.3346723 0.3017738 0.2625735 0.2168333 0.1643824 0.1051237 0.0390406 -0.0337983 -0.1132353 -0.1990211 -0.2908140 -0.3881817 -0.4906037 -0.5974778 -0.7081267 -0.8218084 -0.9377277 -1.0550496 -1.1729142 -1.2904527 -1.4068041 -1.5211318 -1.6326299 -1.7402677 -1.8428948 -1.9396463 -2.0299386 -2.1134371 -2.1900192 -2.2597371 -2.3227815 -2.3794476 -2.4301048 -2.4751708 -2.5150894
Tgif1 2.1439933 2.0366318 1.9320509 1.8302014 1.7310339 1.6344987 1.5405458 1.4491253 1.3601872 1.2736814 1.1895579 1.1077670 1.0282588 0.9509840 0.8758935 0.8029382 0.7320699 0.6632404 0.5964022 0.5315080 0.4685112 0.4073659 0.3480264 0.2904479 0.2345862 0.1803975 0.1278389 0.0768682 0.0274437 -0.0204754 -0.0669293 -0.1119574 -0.1555983 -0.1978901 -0.2388699 -0.2785741 -0.3170385 -0.3542979 -0.3903866 -0.4253379 -0.4591846 -0.4919585 -0.5236909 -0.5544122 -0.5841522 -0.6129397 -0.6408032 -0.6677703 -0.6938677 -0.7191217 -0.7435548 -0.7671243 -0.7897362 -0.8113088 -0.8317743 -0.8510769 -0.8691709 -0.8860190 -0.9015905 -0.9158596 -0.9288035 -0.9404006 -0.9506291 -0.9594650 -0.9668803 -0.9728413 -0.9773066 -0.9802249 -0.9815328 -0.9811523 -0.9789877 -0.9749221 -0.9688136 -0.9604904 -0.9497451 -0.9363279 -0.9199383 -0.9002146 -0.8767217 -0.8489355 -0.8162240 -0.7778240 -0.7328113 -0.6800650 -0.6182221 -0.5456213 -0.4602327 -0.3595837 -0.2410453 -0.1019992 0.0604966 0.2497240 0.4692814 0.7230333 1.0150297 1.3493874 1.7301310 2.1609933 2.6451815 3.0000000
Foxp1 1.6557190 1.6060392 1.5567228 1.5077478 1.4590928 1.4107369 1.3626600 1.3148425 1.2672655 1.2199106 1.1727602 1.1257971 1.0790049 1.0323676 0.9858701 0.9394976 0.8932361 0.8470721 0.8009928 0.7549860 0.7090400 0.6631438 0.6172870 0.5714597 0.5256529 0.4798578 0.4340666 0.3882719 0.3424670 0.2966457 0.2508025 0.2049325 0.1590316 0.1130960 0.0671227 0.0211094 -0.0249458 -0.0710440 -0.1171858 -0.1633711 -0.2095991 -0.2558687 -0.3021778 -0.3485241 -0.3949042 -0.4413147 -0.4877511 -0.5342086 -0.5806816 -0.6271643 -0.6736432 -0.7199615 -0.7658355 -0.8109918 -0.8551725 -0.8981347 -0.9396499 -0.9795026 -1.0174892 -1.0534171 -1.0871025 -1.1183692 -1.1470465 -1.1729677 -1.1959676 -1.2158806 -1.2325383 -1.2457670 -1.2553848 -1.2611993 -1.2630039 -1.2605749 -1.2536677 -1.2420127 -1.2253111 -1.2032300 -1.1753968 -1.1413933 -1.1007489 -1.0529329 -0.9973460 -0.9333101 -0.8600580 -0.7767204 -0.6823120 -0.5757159 -0.4556652 -0.3207404 -0.1698787 -0.0025627 0.1816901 0.3833365 0.6027817 0.8403502 1.0962574 1.3705784 1.6632177 1.9738789 2.3020362 2.6469083
Creb5 2.1349100 2.0546172 1.9755574 1.8977084 1.8210484 1.7455560 1.6712105 1.5979915 1.5258792 1.4548542 1.3848976 1.3159909 1.2481160 1.1812553 1.1153916 1.0505081 0.9865884 0.9236165 0.8615768 0.8004539 0.7402330 0.6808996 0.6224394 0.5648385 0.5080834 0.4521610 0.3970582 0.3427626 0.2892617 0.2365436 0.1845966 0.1334091 0.0829701 0.0332686 -0.0157062 -0.0639645 -0.1115166 -0.1583724 -0.2045417 -0.2500339 -0.2948583 -0.3390240 -0.3825399 -0.4254146 -0.4676565 -0.5092741 -0.5502754 -0.5906683 -0.6304606 -0.6696598 -0.7082688 -0.7461926 -0.7832517 -0.8192775 -0.8541147 -0.8876210 -0.9196653 -0.9501269 -0.9788939 -1.0058621 -1.0309331 -1.0540132 -1.0750113 -1.0938378 -1.1104026 -1.1246130 -1.1363723 -1.1455777 -1.1521179 -1.1558709 -1.1567016 -1.1544592 -1.1489737 -1.1400531 -1.1274791 -1.1110032 -1.0903417 -1.0651702 -1.0351168 -0.9997552 -0.9585957 -0.9110750 -0.8565450 -0.7942584 -0.7233527 -0.6428314 -0.5515411 -0.4481582 -0.3315589 -0.2009699 -0.0555918 0.1054097 0.2828846 0.4776757 0.6905926 0.9223810 1.1736884 1.4450252 1.7367229 2.0488892
Jund 1.8228545 1.7698572 1.7170161 1.6643276 1.6117884 1.5593947 1.5071432 1.4550304 1.4030531 1.3512078 1.2994914 1.2479006 1.1964324 1.1450836 1.0938511 1.0427322 0.9917237 0.9408229 0.8900270 0.8393332 0.7887388 0.7382412 0.6878379 0.6375263 0.5873040 0.5371686 0.4871178 0.4371494 0.3872611 0.3374509 0.2877166 0.2380563 0.1884680 0.1389499 0.0895002 0.0401171 -0.0092010 -0.0584558 -0.1076486 -0.1567811 -0.2058545 -0.2548703 -0.3038295 -0.3527335 -0.4015833 -0.4503799 -0.4991242 -0.5478172 -0.5964597 -0.6450523 -0.6935896 -0.7419359 -0.7898343 -0.8370276 -0.8832637 -0.9282952 -0.9718796 -1.0137784 -1.0537572 -1.0915853 -1.1270348 -1.1598804 -1.1898987 -1.2168671 -1.2405635 -1.2607653 -1.2772482 -1.2897855 -1.2981469 -1.3020973 -1.3013957 -1.2957936 -1.2850342 -1.2688506 -1.2469644 -1.2190840 -1.1849035 -1.1441006 -1.0963351 -1.0412473 -0.9784559 -0.9075569 -0.8281213 -0.7396936 -0.6417904 -0.5338984 -0.4154732 -0.2859534 -0.1452241 0.0062696 0.1680244 0.3395044 0.5201350 0.7092985 0.9063304 1.1105170 1.3210929 1.5372408 1.7580911 1.9827225
Msx1 0.6377484 0.6556217 0.6735028 0.6912847 0.7088579 0.7261101 0.7429269 0.7591913 0.7747845 0.7895856 0.8034722 0.8163209 0.8280071 0.8384060 0.8473928 0.8548433 0.8606343 0.8646445 0.8667549 0.8668495 0.8648162 0.8605473 0.8539407 0.8449001 0.8333362 0.8191676 0.8023214 0.7827339 0.7603519 0.7351330 0.7070467 0.6760748 0.6422123 0.6054679 0.5658646 0.5234399 0.4782464 0.4303522 0.3798405 0.3268100 0.2713746 0.2136633 0.1538195 0.0920006 0.0283773 -0.0368675 -0.1035394 -0.1714341 -0.2403386 -0.3100326 -0.3802772 -0.4505705 -0.5202163 -0.5885994 -0.6551946 -0.7195632 -0.7813477 -0.8402650 -0.8960990 -0.9486925 -0.9979391 -1.0437746 -1.0861695 -1.1251206 -1.1606443 -1.1927696 -1.2215313 -1.2469643 -1.2690979 -1.2879497 -1.3035209 -1.3157898 -1.3247063 -1.3301853 -1.3320989 -1.3302679 -1.3244517 -1.3143346 -1.2995110 -1.2794652 -1.2535465 -1.2209377 -1.1806150 -1.1312956 -1.0713714 -0.9988225 -0.9111051 -0.8050235 -0.6771466 -0.5240275 -0.3416581 -0.1254067 0.1299906 0.4304062 0.7822519 1.1923480 1.6677175 2.2152932 2.8415351 3.0000000
Peg3 1.3950153 1.3768095 1.3585907 1.3403065 1.3219051 1.3033353 1.2845462 1.2654875 1.2461095 1.2263628 1.2061986 1.1855689 1.1644261 1.1427233 1.1204142 1.0974534 1.0737961 1.0493983 1.0242169 0.9982096 0.9713352 0.9435534 0.9148250 0.8851117 0.8543767 0.8225842 0.7896999 0.7556906 0.7205247 0.6841722 0.6466044 0.6077945 0.5677173 0.5263495 0.4836695 0.4396577 0.3942966 0.3475708 0.2994670 0.2499740 0.1990832 0.1467882 0.0930851 0.0379725 -0.0185484 -0.0764737 -0.1357970 -0.1965089 -0.2585974 -0.3220474 -0.3868312 -0.4527089 -0.5192490 -0.5860297 -0.6526467 -0.7187143 -0.7838644 -0.8477471 -0.9100296 -0.9703954 -1.0285433 -1.0841865 -1.1370506 -1.1868725 -1.2333983 -1.2763815 -1.3155805 -1.3507572 -1.3816735 -1.4080894 -1.4297602 -1.4464329 -1.4578438 -1.4637148 -1.4637495 -1.4576295 -1.4450103 -1.4255163 -1.3987358 -1.3642158 -1.3214555 -1.2698998 -1.2089321 -1.1378656 -1.0559349 -0.9622856 -0.8559632 -0.7359198 -0.6015769 -0.4529948 -0.2902813 -0.1135720 0.0769513 0.2810436 0.4983787 0.7285321 0.9709647 1.2250072 1.4898461 1.7645113
Hes1 1.5270416 1.5025261 1.4780026 1.4534345 1.4287855 1.4040193 1.3790999 1.3539913 1.3286580 1.3030645 1.2771753 1.2509555 1.2243702 1.1973847 1.1699645 1.1420755 1.1136837 1.0847554 1.0552570 1.0251555 0.9944179 0.9630116 0.9309044 0.8980643 0.8644597 0.8300592 0.7948321 0.7587478 0.7217762 0.6838877 0.6450530 0.6052433 0.5644305 0.5225867 0.4796846 0.4356977 0.3905998 0.3443653 0.2969695 0.2483880 0.1985974 0.1475746 0.0952977 0.0417453 -0.0131032 -0.0692676 -0.1267668 -0.1856187 -0.2458405 -0.3074484 -0.3704486 -0.4346582 -0.4997168 -0.5652621 -0.6309373 -0.6963913 -0.7612788 -0.8252602 -0.8880017 -0.9491747 -1.0084561 -1.0655275 -1.1200752 -1.1717893 -1.2203635 -1.2654942 -1.3068799 -1.3442203 -1.3772158 -1.4055659 -1.4289688 -1.4471198 -1.4597106 -1.4664275 -1.4669506 -1.4609519 -1.4480944 -1.4280299 -1.4003977 -1.3648229 -1.3209145 -1.2682638 -1.2064420 -1.1349988 -1.0534597 -0.9613245 -0.8580648 -0.7431397 -0.6165286 -0.4788488 -0.3307659 -0.1729634 -0.0061478 0.1689471 0.3515562 0.5408799 0.7360812 0.9362840 1.1405711 1.3479837
Jun -0.2299473 -0.1659870 -0.1019971 -0.0380964 0.0255949 0.0889557 0.1518637 0.2141958 0.2758280 0.3366353 0.3964919 0.4552710 0.5128454 0.5690868 0.6238666 0.6770553 0.7285232 0.7781400 0.8257749 0.8712971 0.9145753 0.9554783 0.9938747 1.0296333 1.0626229 1.0927126 1.1197720 1.1436709 1.1642799 1.1814701 1.1951135 1.2050831 1.2112529 1.2134980 1.2116949 1.2057218 1.1954582 1.1807857 1.1615875 1.1377494 1.1091593 1.0757074 1.0372871 0.9937943 0.9451284 0.8911918 0.8318909 0.7671358 0.6968407 0.6209245 0.5393272 0.4523487 0.3606283 0.2648146 0.1655514 0.0634760 -0.0407812 -0.1465971 -0.2533571 -0.3604552 -0.4672942 -0.5732864 -0.6778533 -0.7804258 -0.8804439 -0.9773565 -1.0706207 -1.1597015 -1.2440709 -1.3232071 -1.3965930 -1.4637155 -1.5240640 -1.5771286 -1.6223985 -1.6593604 -1.6874962 -1.7062809 -1.7151807 -1.7136502 -1.7011299 -1.6770438 -1.6407968 -1.5917715 -1.5293256 -1.4527894 -1.3614621 -1.2546354 -1.1323688 -0.9956466 -0.8455124 -0.6830225 -0.5092526 -0.3253024 -0.1323006 0.0685918 0.2761784 0.4892262 0.7064635 0.9265802
Mafb 1.4075855 1.3983572 1.3890850 1.3797053 1.3701554 1.3603731 1.3502966 1.3398650 1.3290180 1.3176962 1.3058409 1.2933942 1.2802995 1.2665010 1.2519443 1.2365760 1.2203443 1.2031989 1.1850910 1.1659736 1.1458017 1.1245322 1.1021242 1.0785391 1.0537407 1.0276955 1.0003727 0.9717444 0.9417856 0.9104747 0.8777931 0.8437259 0.8082617 0.7713927 0.7331151 0.6934286 0.6523374 0.6098493 0.5659766 0.5207357 0.4741471 0.4262358 0.3770308 0.3265657 0.2748781 0.2220098 0.1680071 0.1129198 0.0568022 -0.0002880 -0.0582827 -0.1169799 -0.1760635 -0.2352331 -0.2942098 -0.3527360 -0.4105758 -0.4675137 -0.5233549 -0.5779235 -0.6310625 -0.6826320 -0.7325082 -0.7805822 -0.8267586 -0.8709540 -0.9130960 -0.9531212 -0.9909743 -1.0266064 -1.0599737 -1.0910359 -1.1197553 -1.1460946 -1.1700164 -1.1914810 -1.2104457 -1.2268625 -1.2406773 -1.2518279 -1.2602424 -1.2658372 -1.2685155 -1.2681644 -1.2646531 -1.2578299 -1.2475191 -1.2335241 -1.2158079 -1.1945361 -1.1698771 -1.1419959 -1.1110582 -1.0772361 -1.0407122 -1.0016845 -0.9603701 -0.9170097 -0.8718711 -0.8252529
Smarca1 0.9527755 0.9684955 0.9841820 0.9997492 1.0151098 1.0301758 1.0448581 1.0590665 1.0727101 1.0856972 1.0979353 1.1093316 1.1197926 1.1292248 1.1375346 1.1446285 1.1504133 1.1547965 1.1576864 1.1589923 1.1586249 1.1564965 1.1525215 1.1466162 1.1386999 1.1286945 1.1165252 1.1021209 1.0854145 1.0663430 1.0448482 1.0208770 0.9943817 0.9653202 0.9336567 0.8993618 0.8624129 0.8227945 0.7804986 0.7355246 0.6878804 0.6375815 0.5846522 0.5291252 0.4710421 0.4104531 0.3474174 0.2820030 0.2142869 0.1443549 0.0723116 -0.0015147 -0.0766040 -0.1524567 -0.2286045 -0.3046110 -0.3800722 -0.4546167 -0.5279048 -0.5996277 -0.6695067 -0.7372907 -0.8027554 -0.8657004 -0.9259477 -0.9833390 -1.0377332 -1.0890041 -1.1370379 -1.1817302 -1.2229839 -1.2607058 -1.2948045 -1.3251872 -1.3517571 -1.3744102 -1.3930324 -1.4074960 -1.4176565 -1.4233487 -1.4243824 -1.4205385 -1.4115632 -1.3971630 -1.3769980 -1.3506747 -1.3177376 -1.2776706 -1.2302300 -1.1755357 -1.1137144 -1.0448879 -0.9691855 -0.8867554 -0.7977758 -0.7024675 -0.6011050 -0.4940283 -0.3816547 -0.2644893
Camta1 1.9425858 1.8980164 1.8535802 1.8092645 1.7650564 1.7209435 1.6769135 1.6329542 1.5890535 1.5451998 1.5013811 1.4575862 1.4138036 1.3700221 1.3262307 1.2824186 1.2385751 1.1946897 1.1507521 1.1067521 1.0626798 1.0185252 0.9742787 0.9299310 0.8854726 0.8408946 0.7961878 0.7513437 0.7063537 0.6612093 0.6159024 0.5704249 0.5247692 0.4789274 0.4328924 0.3866567 0.3402134 0.2935558 0.2466770 0.1995709 0.1522311 0.1046517 0.0568269 0.0087512 -0.0395808 -0.0881742 -0.1370339 -0.1861645 -0.2355705 -0.2852560 -0.3352208 -0.3853731 -0.4355362 -0.4855330 -0.5351901 -0.5843373 -0.6328078 -0.6804383 -0.7270683 -0.7725405 -0.8167005 -0.8593965 -0.9004791 -0.9398009 -0.9772168 -1.0125830 -1.0457570 -1.0765974 -1.1049633 -1.1307137 -1.1537077 -1.1738035 -1.1908581 -1.2047270 -1.2152633 -1.2223172 -1.2257359 -1.2253624 -1.2210351 -1.2125871 -1.1998453 -1.1826302 -1.1607542 -1.1340217 -1.1022275 -1.0651562 -1.0225811 -0.9742719 -0.9202595 -0.8608907 -0.7965323 -0.7275558 -0.6543392 -0.5772690 -0.4967422 -0.4131672 -0.3269660 -0.2385749 -0.1484453 -0.0570451
E2f5 1.8562881 1.8165953 1.7770033 1.7375020 1.6980815 1.6587318 1.6194432 1.5802061 1.5410110 1.5018485 1.4627093 1.4235841 1.3844639 1.3453398 1.3062028 1.2670443 1.2278557 1.1886283 1.1493538 1.1100239 1.0706305 1.0311655 0.9916209 0.9519890 0.9122619 0.8724322 0.8324924 0.7924352 0.7522532 0.7119395 0.6714870 0.6308889 0.5901386 0.5492293 0.5081546 0.4669083 0.4254841 0.3838760 0.3420780 0.3000843 0.2578893 0.2154875 0.1728735 0.1300422 0.0869883 0.0437070 0.0001935 -0.0435568 -0.0875485 -0.1317858 -0.1762703 -0.2209488 -0.2657165 -0.3104682 -0.3551003 -0.3995109 -0.4435996 -0.4872679 -0.5304185 -0.5729561 -0.6147865 -0.6558172 -0.6959571 -0.7351162 -0.7732060 -0.8101390 -0.8458288 -0.8801898 -0.9131376 -0.9445882 -0.9744582 -1.0026648 -1.0291255 -1.0537578 -1.0764793 -1.0972076 -1.1158596 -1.1323520 -1.1466005 -1.1585203 -1.1680249 -1.1750271 -1.1794375 -1.1811654 -1.1801177 -1.1761992 -1.1693121 -1.1593605 -1.1463978 -1.1306536 -1.1123665 -1.0917752 -1.0691186 -1.0446365 -1.0185701 -0.9911624 -0.9626587 -0.9333065 -0.9033562 -0.8730609
Dmrtb1 1.8338638 1.8052919 1.7768570 1.7484327 1.7198971 1.6911332 1.6620292 1.6324782 1.6023785 1.5716339 1.5401538 1.5078536 1.4746549 1.4404857 1.4052808 1.3689824 1.3315400 1.2929108 1.2530605 1.2119629 1.1696008 1.1259658 1.0810587 1.0348900 0.9874794 0.9388566 0.8890605 0.8381400 0.7861533 0.7331680 0.6792608 0.6245169 0.5690301 0.5129017 0.4562402 0.3991606 0.3417838 0.2842354 0.2266451 0.1691456 0.1118716 0.0549589 -0.0014569 -0.0572412 -0.1122619 -0.1663903 -0.2195019 -0.2714779 -0.3222059 -0.3715807 -0.4195004 -0.4657708 -0.5101448 -0.5524332 -0.5925035 -0.6302734 -0.6657041 -0.6987939 -0.7295719 -0.7580921 -0.7844279 -0.8086673 -0.8309087 -0.8512568 -0.8698202 -0.8867076 -0.9020269 -0.9158826 -0.9283745 -0.9395971 -0.9496383 -0.9585791 -0.9664929 -0.9734455 -0.9794944 -0.9846890 -0.9890700 -0.9926693 -0.9955094 -0.9976030 -0.9989523 -0.9995478 -0.9993670 -0.9983729 -0.9965112 -0.9937076 -0.9898639 -0.9848543 -0.9785746 -0.9709596 -0.9619291 -0.9513872 -0.9392244 -0.9253208 -0.9095493 -0.8917805 -0.8718879 -0.8497554 -0.8252851 -0.7984082
Insm2 3.0000000 3.0000000 0.9472274 0.2060407 -0.0320474 -0.1078657 -0.1320253 -0.1397585 -0.1422501 -0.1430594 -0.1433248 -0.1434127 -0.1434422 -0.1434522 -0.1434557 -0.1434569 -0.1434573 -0.1434575 -0.1434575 -0.1434575 -0.1434575 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434576 -0.1434575 -0.1434575 -0.1434575 -0.1434575 -0.1434574 -0.1434572 -0.1434568 -0.1434560 -0.1434543 -0.1434513 -0.1434458 -0.1434365 -0.1434217 -0.1433998 -0.1433698 -0.1433325 -0.1432910 -0.1432512 -0.1432209 -0.1432073 -0.1432147 -0.1432422 -0.1432839 -0.1433307 -0.1433735 -0.1434066 -0.1434291 -0.1434428 -0.1434504 -0.1434543 -0.1434561 -0.1434570 -0.1434573 -0.1434575 -0.1434575 -0.1434575
Ptf1a 3.0000000 3.0000000 2.6091697 1.3486412 0.6377661 0.2497108 0.0415442 -0.0692320 -0.1280417 -0.1592946 -0.1759552 -0.1848774 -0.1896825 -0.1922873 -0.1937096 -0.1944925 -0.1949271 -0.1951707 -0.1953085 -0.1953874 -0.1954330 -0.1954597 -0.1954755 -0.1954850 -0.1954907 -0.1954943 -0.1954965 -0.1954979 -0.1954988 -0.1954994 -0.1954998 -0.1955001 -0.1955002 -0.1955004 -0.1955005 -0.1955005 -0.1955006 -0.1955006 -0.1955006 -0.1955006 -0.1955007 -0.1955007 -0.1955007 -0.1955007 -0.1955007 -0.1955007 -0.1955007 -0.1955006 -0.1955006 -0.1955006 -0.1955005 -0.1955005 -0.1955004 -0.1955002 -0.1955000 -0.1954997 -0.1954991 -0.1954983 -0.1954970 -0.1954950 -0.1954918 -0.1954865 -0.1954782 -0.1954647 -0.1954431 -0.1954087 -0.1953541 -0.1952684 -0.1951354 -0.1949323 -0.1946274 -0.1941792 -0.1935360 -0.1926378 -0.1914219 -0.1898330 -0.1878383 -0.1854466 -0.1827279 -0.1798286 -0.1769735 -0.1744496 -0.1725675 -0.1716051 -0.1717444 -0.1730215 -0.1753049 -0.1783140 -0.1816371 -0.1848554 -0.1876848 -0.1899890 -0.1917508 -0.1930283 -0.1939138 -0.1945048 -0.1948868 -0.1951273 -0.1952756 -0.1953657
Neurod4 3.0000000 3.0000000 1.9479342 0.8438916 0.3106099 0.0549915 -0.0672504 -0.1257465 -0.1538059 -0.1673140 -0.1738463 -0.1770219 -0.1785750 -0.1793397 -0.1797189 -0.1799085 -0.1800041 -0.1800528 -0.1800778 -0.1800908 -0.1800976 -0.1801012 -0.1801031 -0.1801042 -0.1801048 -0.1801051 -0.1801053 -0.1801054 -0.1801055 -0.1801055 -0.1801055 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801056 -0.1801055 -0.1801055 -0.1801055 -0.1801055 -0.1801054 -0.1801052 -0.1801050 -0.1801047 -0.1801041 -0.1801031 -0.1801015 -0.1800989 -0.1800944 -0.1800869 -0.1800746 -0.1800543 -0.1800210 -0.1799669 -0.1798799 -0.1797416 -0.1795242 -0.1791874 -0.1786736 -0.1779032 -0.1767699 -0.1751304 -0.1727899 -0.1694863 -0.1648690 -0.1584689 -0.1496575 -0.1375897 -0.1211233 -0.0987058 -0.0682118 -0.0267085 0.0298841 
write.table(heatmap_matrix_q_value_5_10_minus_5, file = file.path(tables_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
2.2.2.1.2 q value < 0.01
significant_genes_q_value_0.01 <- filter(diff_test_res_all_genes, qval < 0.01) %>% .$gene 
cat("Number of significant genes: ", length(significant_genes_q_value_0.01))
## Number of significant genes:  7245
significant_transcription_factors_q_value_0.01 <- as.character(significant_genes_q_value_0.01[significant_genes_q_value_0.01 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_0.01))
## Number of significant transcription factors: 474
plot_genes_heatmap_output_q_value_0.01 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)

## <simpleError in checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon): NAs found in the working weights variable 'wz'>
save_pheatmap_pdf(plot_genes_heatmap_output_q_value_0.01[[2]], file.path("figures", "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11", "diff_test_plots_transcription_factors_only_q_value_0.01_heatmap_custom.pdf"), width=16, height=40)
## pdf 
##   2
heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
ph_res_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[2]]
pheatmap_ordering_q_value_0.01 <- rownames(heatmap_matrix_q_value_0.01[ph_res_q_value_0.01$tree_row[["order"]],])

transcription_factors_table_q_value_0.01 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_0.01)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_0.01 <- transcription_factors_table_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))

write.table(transcription_factors_table_q_value_0.01, file.path(tables_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11-significant_transcription_factors_diff_test_analysis_qval_0.01.txt"), sep="\t", quote=FALSE, row.names=FALSE)

heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
heatmap_matrix_q_value_0.01 <- as.data.frame(heatmap_matrix_q_value_0.01) %>% rownames_to_column("gene")
heatmap_matrix_q_value_0.01 <- heatmap_matrix_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
heatmap_matrix_q_value_0.01 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")
gene 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
Thra 0.0809763 0.1142869 0.1475813 0.1808113 0.2139285 0.2468843 0.2796298 0.3121161 0.3442939 0.3761141 0.4075270 0.4384831 0.4689325 0.4988254 0.5281115 0.5567408 0.5846629 0.6118274 0.6381837 0.6636812 0.6882693 0.7118971 0.7345138 0.7560687 0.7765107 0.7957891 0.8138530 0.8306514 0.8461337 0.8602490 0.8729467 0.8841761 0.8938869 0.9020286 0.9085512 0.9134045 0.9165388 0.9179046 0.9174524 0.9151333 0.9108985 0.9046994 0.8964881 0.8862167 0.8738381 0.8593052 0.8425716 0.8235914 0.8023192 0.7787101 0.7527217 0.7243532 0.6936439 0.6606345 0.6253665 0.5878815 0.5482214 0.5064283 0.4625446 0.4166130 0.3686763 0.3187776 0.2669599 0.2132666 0.1577411 0.1004269 0.0413676 -0.0193930 -0.0818114 -0.1458437 -0.2114463 -0.2785753 -0.3471871 -0.4172380 -0.4886845 -0.5614829 -0.6355898 -0.7109620 -0.7875561 -0.8653291 -0.9442382 -1.0242404 -1.1052932 -1.1873543 -1.2703814 -1.3543325 -1.4391660 -1.5248395 -1.6112885 -1.6984223 -1.7861496 -1.8743802 -1.9630245 -2.0519940 -2.1412011 -2.2305591 -2.3199823 -2.4093860 -2.4986864 -2.5878008
Zfp706 -0.0765897 -0.0367229 0.0031568 0.0429950 0.0827369 0.1223276 0.1617117 0.2008333 0.2396363 0.2780644 0.3160609 0.3535686 0.3905303 0.4268884 0.4625849 0.4975617 0.5317605 0.5651226 0.5975893 0.6291017 0.6596006 0.6890267 0.7173207 0.7444232 0.7702746 0.7948153 0.8179860 0.8397269 0.8599787 0.8786819 0.8957773 0.9112057 0.9249083 0.9368263 0.9469012 0.9550749 0.9612896 0.9654879 0.9676127 0.9676074 0.9654160 0.9609831 0.9542536 0.9451735 0.9336891 0.9197476 0.9032970 0.8842863 0.8626651 0.8383843 0.8113982 0.7817161 0.7494001 0.7145148 0.6771253 0.6372972 0.5950965 0.5505898 0.5038436 0.4549249 0.4039011 0.3508394 0.2958074 0.2388727 0.1801030 0.1195658 0.0573289 -0.0065404 -0.0719745 -0.1389063 -0.2072688 -0.2769951 -0.3480188 -0.4202737 -0.4936939 -0.5682139 -0.6437688 -0.7202938 -0.7977250 -0.8759986 -0.9550516 -1.0348215 -1.1152463 -1.1962648 -1.2778162 -1.3598406 -1.4422786 -1.5250717 -1.6081603 -1.6914843 -1.7749841 -1.8586009 -1.9422770 -2.0259553 -2.1095796 -2.1930948 -2.2764465 -2.3595812 -2.4424465 -2.5249907
Zfp760 1.1988863 1.1871660 1.1754425 1.1636969 1.1519101 1.1400631 1.1281373 1.1161138 1.1039743 1.0917001 1.0792730 1.0666747 1.0538872 1.0408924 1.0276726 1.0142101 1.0004873 0.9864867 0.9721912 0.9575837 0.9426472 0.9273649 0.9117203 0.8956970 0.8792789 0.8624499 0.8451942 0.8274964 0.8093410 0.7907131 0.7715978 0.7519805 0.7318469 0.7111831 0.6899752 0.6682099 0.6458741 0.6229550 0.5994401 0.5753174 0.5505750 0.5252017 0.4991864 0.4725185 0.4451880 0.4171849 0.3884999 0.3591243 0.3290494 0.2982674 0.2667706 0.2345494 0.2015924 0.1678887 0.1334280 0.0982006 0.0621974 0.0254103 -0.0121685 -0.0505459 -0.0897281 -0.1297207 -0.1705283 -0.2121551 -0.2546041 -0.2978778 -0.3419779 -0.3869051 -0.4326594 -0.4792400 -0.5266452 -0.5748725 -0.6239184 -0.6737786 -0.7244480 -0.7759206 -0.8281894 -0.8812465 -0.9350834 -0.9896903 -1.0450568 -1.1011715 -1.1580221 -1.2155953 -1.2738771 -1.3328527 -1.3925060 -1.4528189 -1.5137195 -1.5750770 -1.6367613 -1.6986471 -1.7606136 -1.8225447 -1.8843290 -1.9458598 -2.0070354 -2.0677582 -2.1279357 -2.1874796
Id1 1.4871422 1.4381725 1.3894833 1.3411226 1.2931377 1.2455749 1.1984795 1.1518958 1.1058674 1.0604368 1.0156456 0.9715347 0.9281439 0.8855122 0.8436780 0.8026786 0.7625507 0.7233304 0.6850529 0.6477527 0.6114640 0.5762202 0.5420543 0.5089987 0.4770855 0.4463464 0.4168129 0.3885160 0.3614870 0.3357566 0.3113557 0.2883152 0.2666661 0.2464396 0.2276672 0.2103805 0.1946119 0.1803940 0.1677600 0.1567441 0.1473808 0.1397059 0.1337558 0.1295683 0.1271821 0.1266372 0.1279752 0.1312388 0.1364727 0.1437230 0.1530277 0.1642137 0.1769041 0.1907122 0.2052487 0.2201220 0.2349368 0.2492952 0.2627959 0.2750354 0.2856078 0.2941061 0.3001230 0.3032521 0.3030896 0.2992353 0.2912950 0.2788825 0.2616214 0.2391483 0.2111148 0.1771908 0.1370677 0.0904614 0.0371163 -0.0231912 -0.0906488 -0.1654039 -0.2475593 -0.3371692 -0.4342341 -0.5386972 -0.6504391 -0.7692745 -0.8949478 -1.0271304 -1.1654176 -1.3093116 -1.4577780 -1.6092531 -1.7622270 -1.9152926 -2.0671595 -2.2166656 -2.3627842 -2.5046291 -2.6414553 -2.7726568 -2.8977616 -3.0000000
Msx2 1.2595102 1.2236724 1.1881777 1.1530591 1.1183487 1.0840771 1.0502741 1.0169680 0.9841864 0.9519556 0.9203010 0.8892473 0.8588179 0.8290356 0.7999225 0.7714997 0.7437877 0.7168065 0.6905755 0.6651133 0.6404384 0.6165687 0.5935217 0.5713147 0.5499647 0.5294887 0.5099033 0.4912253 0.4734715 0.4566586 0.4408036 0.4259237 0.4120364 0.3991596 0.3873115 0.3765109 0.3667772 0.3581305 0.3505915 0.3441820 0.3389245 0.3348426 0.3319609 0.3303056 0.3299037 0.3307839 0.3329766 0.3365135 0.3414283 0.3477566 0.3555239 0.3644971 0.3741921 0.3841093 0.3937433 0.4025829 0.4101117 0.4158099 0.4191568 0.4196341 0.4167297 0.4099428 0.3987892 0.3828077 0.3615669 0.3346723 0.3017738 0.2625735 0.2168333 0.1643824 0.1051237 0.0390406 -0.0337983 -0.1132353 -0.1990211 -0.2908140 -0.3881817 -0.4906037 -0.5974778 -0.7081267 -0.8218084 -0.9377277 -1.0550496 -1.1729142 -1.2904527 -1.4068041 -1.5211318 -1.6326299 -1.7402677 -1.8428948 -1.9396463 -2.0299386 -2.1134371 -2.1900192 -2.2597371 -2.3227815 -2.3794476 -2.4301048 -2.4751708 -2.5150894
Pitx3 -0.4367448 -0.4044712 -0.3631641 -0.3106588 -0.2444708 -0.1618466 -0.0598691 0.0643629 0.2134704 0.3894350 0.5931541 0.8239338 1.0789679 1.3528796 1.6374201 1.9214327 2.1911818 2.4311121 2.6250464 2.7577470 2.8166765 2.7937163 2.6865517 2.4994409 2.2431577 1.9340245 1.5921304 1.2389970 0.8950870 0.5775932 0.2988844 0.0658297 -0.1199800 -0.2612864 -0.3637950 -0.4347155 -0.4814913 -0.5108860 -0.5284743 -0.5384872 -0.5439060 -0.5466913 -0.5480499 -0.5486780 -0.5489530 -0.5490669 -0.5491115 -0.5491280 -0.5491337 -0.5491356 -0.5491362 -0.5491363 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491364 -0.5491363 -0.5491356 -0.5491155 -0.5485856 -0.5340411 -0.1280237
Jun -0.2299473 -0.1659870 -0.1019971 -0.0380964 0.0255949 0.0889557 0.1518637 0.2141958 0.2758280 0.3366353 0.3964919 0.4552710 0.5128454 0.5690868 0.6238666 0.6770553 0.7285232 0.7781400 0.8257749 0.8712971 0.9145753 0.9554783 0.9938747 1.0296333 1.0626229 1.0927126 1.1197720 1.1436709 1.1642799 1.1814701 1.1951135 1.2050831 1.2112529 1.2134980 1.2116949 1.2057218 1.1954582 1.1807857 1.1615875 1.1377494 1.1091593 1.0757074 1.0372871 0.9937943 0.9451284 0.8911918 0.8318909 0.7671358 0.6968407 0.6209245 0.5393272 0.4523487 0.3606283 0.2648146 0.1655514 0.0634760 -0.0407812 -0.1465971 -0.2533571 -0.3604552 -0.4672942 -0.5732864 -0.6778533 -0.7804258 -0.8804439 -0.9773565 -1.0706207 -1.1597015 -1.2440709 -1.3232071 -1.3965930 -1.4637155 -1.5240640 -1.5771286 -1.6223985 -1.6593604 -1.6874962 -1.7062809 -1.7151807 -1.7136502 -1.7011299 -1.6770438 -1.6407968 -1.5917715 -1.5293256 -1.4527894 -1.3614621 -1.2546354 -1.1323688 -0.9956466 -0.8455124 -0.6830225 -0.5092526 -0.3253024 -0.1323006 0.0685918 0.2761784 0.4892262 0.7064635 0.9265802
Lmx1a 0.4676597 0.5002755 0.5331323 0.5661477 0.5992363 0.6323092 0.6652744 0.6980363 0.7304966 0.7625533 0.7941017 0.8250340 0.8552397 0.8846057 0.9130165 0.9403547 0.9665007 0.9913338 1.0147320 1.0365725 1.0567323 1.0750885 1.0915188 1.1059020 1.1181188 1.1280519 1.1355873 1.1406140 1.1430254 1.1427198 1.1396008 1.1335781 1.1245684 1.1124957 1.0972922 1.0788989 1.0572662 1.0323545 1.0041346 0.9725887 0.9377103 0.8995049 0.8579906 0.8131977 0.7651697 0.7139631 0.6596472 0.6023048 0.5420313 0.4789350 0.4131449 0.3449714 0.2748797 0.2033206 0.1307214 0.0574839 -0.0160165 -0.0894320 -0.1624422 -0.2347543 -0.3061029 -0.3762490 -0.4449794 -0.5121054 -0.5774614 -0.6409037 -0.7023090 -0.7615725 -0.8186066 -0.8733389 -0.9257109 -0.9756762 -1.0231988 -1.0682514 -1.1108143 -1.1508734 -1.1884190 -1.2234445 -1.2559446 -1.2859143 -1.3133475 -1.3382357 -1.3605665 -1.3803226 -1.3974804 -1.4120082 -1.4238652 -1.4330045 -1.4395131 -1.4436328 -1.4455994 -1.4456364 -1.4439587 -1.4407747 -1.4362896 -1.4307073 -1.4242321 -1.4170701 -1.4094312 -1.4015289
Smad6 0.0598186 0.1088869 0.1587385 0.2092800 0.2604107 0.3120222 0.3639986 0.4162159 0.4685423 0.5208379 0.5729549 0.6247374 0.6760218 0.7266370 0.7764047 0.8251395 0.8726499 0.9187384 0.9632023 1.0058345 1.0464244 1.0847587 1.1206224 1.1538001 1.1840772 1.2112410 1.2350822 1.2553966 1.2719861 1.2846606 1.2932397 1.2975538 1.2974465 1.2927755 1.2834147 1.2692556 1.2502085 1.2262046 1.1971966 1.1631605 1.1240961 1.0800283 1.0310075 0.9771106 0.9184406 0.8551272 0.7873264 0.7152200 0.6390153 0.5589435 0.4752726 0.3885714 0.2996545 0.2092960 0.1182133 0.0270635 -0.0635575 -0.1531159 -0.2411387 -0.3272122 -0.4109790 -0.4921352 -0.5704263 -0.6456433 -0.7176184 -0.7862206 -0.8513512 -0.9129393 -0.9709378 -1.0253189 -1.0760704 -1.1231915 -1.1666894 -1.2065760 -1.2428639 -1.2755637 -1.3046809 -1.3302123 -1.3521434 -1.3704447 -1.3850687 -1.3959461 -1.4029820 -1.4060512 -1.4049936 -1.3996082 -1.3896463 -1.3748122 -1.3550099 -1.3304038 -1.3011494 -1.2673872 -1.2292523 -1.1868844 -1.1404374 -1.0900892 -1.0360511 -0.9785771 -0.9179740 -0.8546094
Klf10 -0.0366176 0.0157093 0.0685285 0.1217438 0.1752548 0.2289564 0.2827391 0.3364886 0.3900865 0.4434095 0.4963302 0.5487166 0.6004328 0.6513385 0.7012900 0.7501396 0.7977363 0.8439263 0.8885528 0.9314568 0.9724773 1.0114518 1.0482168 1.0826084 1.1144627 1.1436165 1.1699077 1.1931765 1.2132655 1.2300205 1.2432918 1.2529343 1.2588084 1.2607812 1.2587267 1.2525273 1.2420739 1.2272672 1.2080184 1.1842497 1.1558954 1.1229027 1.0852318 1.0428572 0.9957681 0.9439688 0.8874793 0.8263359 0.7605910 0.6903142 0.6156043 0.5368436 0.4546648 0.3696913 0.2825231 0.1937338 0.1038689 0.0134436 -0.0770575 -0.1671815 -0.2565071 -0.3446443 -0.4312334 -0.5159445 -0.5984758 -0.6785521 -0.7559229 -0.8303608 -0.9016590 -0.9696292 -1.0340994 -1.0949113 -1.1519179 -1.2049810 -1.2539685 -1.2987516 -1.3392026 -1.3751915 -1.4065834 -1.4332356 -1.4549941 -1.4716905 -1.4831384 -1.4891297 -1.4894301 -1.4837750 -1.4718640 -1.4533672 -1.4282666 -1.3969295 -1.3597295 -1.3170317 -1.2692009 -1.2166094 -1.1596445 -1.0987150 -1.0342575 -0.9667421 -0.8966775 -0.8246155
Ets1 1.8481815 1.8067570 1.7656250 1.7247655 1.6841594 1.6437877 1.6036321 1.5636750 1.5238990 1.4842876 1.4448244 1.4054937 1.3662805 1.3271700 1.2881481 1.2492009 1.2103154 1.1714788 1.1326788 1.0939037 1.0551422 1.0163836 0.9776175 0.9388340 0.9000239 0.8611783 0.8222887 0.7833473 0.7443465 0.7052795 0.6661397 0.6269211 0.5876182 0.5482259 0.5087397 0.4691554 0.4294694 0.3896786 0.3497802 0.3097721 0.2696525 0.2294201 0.1890742 0.1486145 0.1080410 0.0673544 0.0265557 -0.0143535 -0.0553713 -0.0964953 -0.1377205 -0.1789994 -0.2202461 -0.2613768 -0.3023113 -0.3429731 -0.3832895 -0.4231913 -0.4626127 -0.5014915 -0.5397685 -0.5773881 -0.6142972 -0.6504462 -0.6857877 -0.7202773 -0.7538729 -0.7865345 -0.8182246 -0.8489072 -0.8785483 -0.9071153 -0.9345771 -0.9609035 -0.9860657 -1.0100353 -1.0327845 -1.0542862 -1.0745130 -1.0934378 -1.1110329 -1.1272705 -1.1421218 -1.1555570 -1.1675453 -1.1780543 -1.1870500 -1.1944988 -1.2004425 -1.2050110 -1.2083355 -1.2105447 -1.2117650 -1.2121214 -1.2117376 -1.2107366 -1.2092412 -1.2073741 -1.2052581 -1.2030164
Mta3 1.9442808 1.8952440 1.8464660 1.7979498 1.7496986 1.7017151 1.6540022 1.6065628 1.5593993 1.5125144 1.4659107 1.4195905 1.3735563 1.3278102 1.2823545 1.2371914 1.1923228 1.1477509 1.1034774 1.0595043 1.0158333 0.9724662 0.9294046 0.8866501 0.8442043 0.8020686 0.7602444 0.7187330 0.6775359 0.6366541 0.5960890 0.5558416 0.5159129 0.4763041 0.4370161 0.3980499 0.3594062 0.3210860 0.2830901 0.2454191 0.2080738 0.1710548 0.1343628 0.0979983 0.0619619 0.0262541 -0.0091246 -0.0441738 -0.0788932 -0.1132823 -0.1473408 -0.1810699 -0.2144716 -0.2475483 -0.2803021 -0.3127354 -0.3448502 -0.3766488 -0.4081334 -0.4393060 -0.4701687 -0.5007237 -0.5309731 -0.5609188 -0.5905630 -0.6199077 -0.6489548 -0.6777063 -0.7061642 -0.7343304 -0.7622069 -0.7897956 -0.8170983 -0.8441168 -0.8708532 -0.8973091 -0.9234863 -0.9493868 -0.9750121 -1.0003642 -1.0254447 -1.0502553 -1.0747977 -1.0990736 -1.1230846 -1.1468325 -1.1703188 -1.1935452 -1.2165200 -1.2392583 -1.2617757 -1.2840874 -1.3062085 -1.3281537 -1.3499378 -1.3715750 -1.3930796 -1.4144655 -1.4357467 -1.4569366
E2f5 1.8562881 1.8165953 1.7770033 1.7375020 1.6980815 1.6587318 1.6194432 1.5802061 1.5410110 1.5018485 1.4627093 1.4235841 1.3844639 1.3453398 1.3062028 1.2670443 1.2278557 1.1886283 1.1493538 1.1100239 1.0706305 1.0311655 0.9916209 0.9519890 0.9122619 0.8724322 0.8324924 0.7924352 0.7522532 0.7119395 0.6714870 0.6308889 0.5901386 0.5492293 0.5081546 0.4669083 0.4254841 0.3838760 0.3420780 0.3000843 0.2578893 0.2154875 0.1728735 0.1300422 0.0869883 0.0437070 0.0001935 -0.0435568 -0.0875485 -0.1317858 -0.1762703 -0.2209488 -0.2657165 -0.3104682 -0.3551003 -0.3995109 -0.4435996 -0.4872679 -0.5304185 -0.5729561 -0.6147865 -0.6558172 -0.6959571 -0.7351162 -0.7732060 -0.8101390 -0.8458288 -0.8801898 -0.9131376 -0.9445882 -0.9744582 -1.0026648 -1.0291255 -1.0537578 -1.0764793 -1.0972076 -1.1158596 -1.1323520 -1.1466005 -1.1585203 -1.1680249 -1.1750271 -1.1794375 -1.1811654 -1.1801177 -1.1761992 -1.1693121 -1.1593605 -1.1463978 -1.1306536 -1.1123665 -1.0917752 -1.0691186 -1.0446365 -1.0185701 -0.9911624 -0.9626587 -0.9333065 -0.9033562 -0.8730609
Dmrtb1 1.8338638 1.8052919 1.7768570 1.7484327 1.7198971 1.6911332 1.6620292 1.6324782 1.6023785 1.5716339 1.5401538 1.5078536 1.4746549 1.4404857 1.4052808 1.3689824 1.3315400 1.2929108 1.2530605 1.2119629 1.1696008 1.1259658 1.0810587 1.0348900 0.9874794 0.9388566 0.8890605 0.8381400 0.7861533 0.7331680 0.6792608 0.6245169 0.5690301 0.5129017 0.4562402 0.3991606 0.3417838 0.2842354 0.2266451 0.1691456 0.1118716 0.0549589 -0.0014569 -0.0572412 -0.1122619 -0.1663903 -0.2195019 -0.2714779 -0.3222059 -0.3715807 -0.4195004 -0.4657708 -0.5101448 -0.5524332 -0.5925035 -0.6302734 -0.6657041 -0.6987939 -0.7295719 -0.7580921 -0.7844279 -0.8086673 -0.8309087 -0.8512568 -0.8698202 -0.8867076 -0.9020269 -0.9158826 -0.9283745 -0.9395971 -0.9496383 -0.9585791 -0.9664929 -0.9734455 -0.9794944 -0.9846890 -0.9890700 -0.9926693 -0.9955094 -0.9976030 -0.9989523 -0.9995478 -0.9993670 -0.9983729 -0.9965112 -0.9937076 -0.9898639 -0.9848543 -0.9785746 -0.9709596 -0.9619291 -0.9513872 -0.9392244 -0.9253208 -0.9095493 -0.8917805 -0.8718879 -0.8497554 -0.8252851 -0.7984082
Klf5 1.1740817 1.1729262 1.1717193 1.1704091 1.1689442 1.1672728 1.1653435 1.1631050 1.1605061 1.1574957 1.1540231 1.1500378 1.1454895 1.1403285 1.1345054 1.1279715 1.1206784 1.1125785 1.1036252 1.0937722 1.0829748 1.0711886 1.0583709 1.0444799 1.0294753 1.0133180 0.9959707 0.9773977 0.9575648 0.9364400 0.9139932 0.8901963 0.8650236 0.8384515 0.8104590 0.7810276 0.7501416 0.7177877 0.6839559 0.6486387 0.6118321 0.5735347 0.5337488 0.4924796 0.4497358 0.4055293 0.3598756 0.3127934 0.2643052 0.2144365 0.1632210 0.1107867 0.0573454 0.0031046 -0.0517363 -0.1069867 -0.1624651 -0.2179991 -0.2734255 -0.3285905 -0.3833496 -0.4375673 -0.4911171 -0.5438811 -0.5957501 -0.6466228 -0.6964055 -0.7450122 -0.7923635 -0.8383866 -0.8830148 -0.9261867 -0.9678461 -1.0079414 -1.0464249 -1.0832526 -1.1183833 -1.1517785 -1.1834015 -1.2132172 -1.2411913 -1.2672901 -1.2914796 -1.3137250 -1.3339905 -1.3522384 -1.3684285 -1.3825213 -1.3945828 -1.4048006 -1.4133611 -1.4204443 -1.4262248 -1.4308726 -1.4345544 -1.4374344 -1.4396748 -1.4414364 -1.4428792 -1.4441624
Maf 1.4928511 1.4743189 1.4557993 1.4372581 1.4186615 1.3999763 1.3811693 1.3622079 1.3430599 1.3236932 1.3040763 1.2841781 1.2639677 1.2434150 1.2224899 1.2011631 1.1794055 1.1571887 1.1344847 1.1112659 1.0875056 1.0631773 1.0382553 1.0127145 0.9865304 0.9596792 0.9321377 0.9038836 0.8748953 0.8451518 0.8146332 0.7833202 0.7511946 0.7182389 0.6844365 0.6497721 0.6142310 0.5777996 0.5404657 0.5022176 0.4630453 0.4229394 0.3818922 0.3398966 0.2969473 0.2530398 0.2081711 0.1623395 0.1155444 0.0677866 0.0190724 -0.0305089 -0.0807915 -0.1316113 -0.1828089 -0.2342298 -0.2857249 -0.3371498 -0.3883657 -0.4392386 -0.4896396 -0.5394448 -0.5885352 -0.6367963 -0.6841183 -0.7303955 -0.7755264 -0.8194133 -0.8619620 -0.9030815 -0.9426838 -0.9806837 -1.0169981 -1.0515458 -1.0842472 -1.1150241 -1.1437988 -1.1704940 -1.1950326 -1.2173366 -1.2373272 -1.2549243 -1.2700456 -1.2826062 -1.2925186 -1.2996910 -1.3040280 -1.3054337 -1.3039610 -1.2998379 -1.2932981 -1.2845727 -1.2738912 -1.2614826 -1.2475764 -1.2324034 -1.2161965 -1.1991914 -1.1816270 -1.1637456
Mafb 1.4075855 1.3983572 1.3890850 1.3797053 1.3701554 1.3603731 1.3502966 1.3398650 1.3290180 1.3176962 1.3058409 1.2933942 1.2802995 1.2665010 1.2519443 1.2365760 1.2203443 1.2031989 1.1850910 1.1659736 1.1458017 1.1245322 1.1021242 1.0785391 1.0537407 1.0276955 1.0003727 0.9717444 0.9417856 0.9104747 0.8777931 0.8437259 0.8082617 0.7713927 0.7331151 0.6934286 0.6523374 0.6098493 0.5659766 0.5207357 0.4741471 0.4262358 0.3770308 0.3265657 0.2748781 0.2220098 0.1680071 0.1129198 0.0568022 -0.0002880 -0.0582827 -0.1169799 -0.1760635 -0.2352331 -0.2942098 -0.3527360 -0.4105758 -0.4675137 -0.5233549 -0.5779235 -0.6310625 -0.6826320 -0.7325082 -0.7805822 -0.8267586 -0.8709540 -0.9130960 -0.9531212 -0.9909743 -1.0266064 -1.0599737 -1.0910359 -1.1197553 -1.1460946 -1.1700164 -1.1914810 -1.2104457 -1.2268625 -1.2406773 -1.2518279 -1.2602424 -1.2658372 -1.2685155 -1.2681644 -1.2646531 -1.2578299 -1.2475191 -1.2335241 -1.2158079 -1.1945361 -1.1698771 -1.1419959 -1.1110582 -1.0772361 -1.0407122 -1.0016845 -0.9603701 -0.9170097 -0.8718711 -0.8252529
Zfp180 1.6338540 1.6091382 1.5844952 1.5598835 1.5352622 1.5105914 1.4858319 1.4609452 1.4358938 1.4106407 1.3851499 1.3593864 1.3333157 1.3069043 1.2801199 1.2529306 1.2253058 1.1972159 1.1686320 1.1395267 1.1098733 1.0796464 1.0488217 1.0173761 0.9852876 0.9525357 0.9191011 0.8849658 0.8501131 0.8145280 0.7781967 0.7411070 0.7032482 0.6646113 0.6251886 0.5849744 0.5439644 0.5021561 0.4595487 0.4161432 0.3719422 0.3269504 0.2811739 0.2346209 0.1873014 0.1392271 0.0904115 0.0408702 -0.0093799 -0.0603195 -0.1119232 -0.1640642 -0.2165263 -0.2691002 -0.3215875 -0.3738011 -0.4255648 -0.4767132 -0.5270914 -0.5765550 -0.6249691 -0.6722083 -0.7181560 -0.7627038 -0.8057509 -0.8472034 -0.8869739 -0.9249801 -0.9611449 -0.9953951 -1.0276606 -1.0578741 -1.0859695 -1.1118820 -1.1355463 -1.1568965 -1.1758647 -1.1923802 -1.2063686 -1.2177506 -1.2264410 -1.2323476 -1.2353699 -1.2353975 -1.2323093 -1.2259713 -1.2162352 -1.2029422 -1.1860980 -1.1659102 -1.1425932 -1.1163598 -1.0874247 -1.0560069 -1.0223328 -0.9866389 -0.9491734 -0.9101992 -0.8699950 -0.8288571
Rbck1 1.0897522 1.0951413 1.1004646 1.1056533 1.1106387 1.1153518 1.1197236 1.1236849 1.1271667 1.1300996 1.1324145 1.1340423 1.1349137 1.1349600 1.1341123 1.1323020 1.1294610 1.1255213 1.1204154 1.1140764 1.1064378 1.0974339 1.0869997 1.0750710 1.0615843 1.0464776 1.0296895 1.0111601 0.9908307 0.9686440 0.9445444 0.9184776 0.8903914 0.8602353 0.8279608 0.7935214 0.7568731 0.7179739 0.6767846 0.6332683 0.5873911 0.5391217 0.4884317 0.4352961 0.3796927 0.3216028 0.2610112 0.1979061 0.1322791 0.0641260 -0.0065435 -0.0794923 -0.1542746 -0.2304475 -0.3075799 -0.3852534 -0.4630627 -0.5406159 -0.6175341 -0.6934518 -0.7680160 -0.8408865 -0.9117346 -0.9802426 -1.0461032 -1.1090182 -1.1686975 -1.2248578 -1.2772217 -1.3255155 -1.3694685 -1.4088108 -1.4432716 -1.4725776 -1.4964509 -1.5146068 -1.5267514 -1.5325796 -1.5317723 -1.5239934 -1.5088875 -1.4860760 -1.4551541 -1.4156868 -1.3672050 -1.3092013 -1.2411248 -1.1623924 -1.0728922 -0.9730990 -0.8635232 -0.7446851 -0.6171227 -0.4813996 -0.3381121 -0.1878959 -0.0314327 0.1305444 0.2972455 0.4678195
Smarca1 0.9527755 0.9684955 0.9841820 0.9997492 1.0151098 1.0301758 1.0448581 1.0590665 1.0727101 1.0856972 1.0979353 1.1093316 1.1197926 1.1292248 1.1375346 1.1446285 1.1504133 1.1547965 1.1576864 1.1589923 1.1586249 1.1564965 1.1525215 1.1466162 1.1386999 1.1286945 1.1165252 1.1021209 1.0854145 1.0663430 1.0448482 1.0208770 0.9943817 0.9653202 0.9336567 0.8993618 0.8624129 0.8227945 0.7804986 0.7355246 0.6878804 0.6375815 0.5846522 0.5291252 0.4710421 0.4104531 0.3474174 0.2820030 0.2142869 0.1443549 0.0723116 -0.0015147 -0.0766040 -0.1524567 -0.2286045 -0.3046110 -0.3800722 -0.4546167 -0.5279048 -0.5996277 -0.6695067 -0.7372907 -0.8027554 -0.8657004 -0.9259477 -0.9833390 -1.0377332 -1.0890041 -1.1370379 -1.1817302 -1.2229839 -1.2607058 -1.2948045 -1.3251872 -1.3517571 -1.3744102 -1.3930324 -1.4074960 -1.4176565 -1.4233487 -1.4243824 -1.4205385 -1.4115632 -1.3971630 -1.3769980 -1.3506747 -1.3177376 -1.2776706 -1.2302300 -1.1755357 -1.1137144 -1.0448879 -0.9691855 -0.8867554 -0.7977758 -0.7024675 -0.6011050 -0.4940283 -0.3816547 -0.2644893 
write.table(heatmap_matrix_q_value_0.01, file = file.path(tables_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11-significant_transcription_factors_diff_test_analysis_qval_0.01_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
2.2.2.1.3 Plotting of transcription factors differentially expressed in pseudotime
2.2.2.1.3.1 Top 10 differentially expressed genes (q value < 5*10^-5)
transcription_factors_table_q_value_5_10_minus_5_ordered_qval <- arrange(transcription_factors_table_q_value_5_10_minus_5, qval)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[1]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[2]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[3]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[4]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[5]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[6]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[7]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[8]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[9]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[10]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

2.3 Selected genes

# Genes of interest.
genes_of_interest <- c("Aqp4", "Fabp7", "Kif9", "Mbp", "Nes", "Pdgfra", "Top2a")

# Remove genes of interest not present in Seurat dataset
genes_not_present <- genes_of_interest[!genes_of_interest %in% rownames(seurat@data)]
genes_of_interest <- genes_of_interest[!genes_of_interest %in% genes_not_present]
if(length(genes_not_present != 0)) {
  print(paste0("The following genes were not present in the Seurat object", genes_not_present))
}
      
diff_test_res <- differentialGeneTest(monocle[genes_of_interest],
      fullModelFormulaStr = "~sm.ns(Pseudotime)")
sig_gene_names <- row.names(subset(diff_test_res, qval < 0.1))
plot_pseudotime_heatmap(monocle[genes_of_interest,],
      num_clusters = 1,
      cores = 1,
      show_rownames = T)

2.3.1 Genes in pseudotime, single branch (Selected genes)

p <- plot_genes_in_pseudotime(monocle[genes_of_interest,], color_by="cluster") + scale_color_manual(values=colours)
p <- p %>% remove_geom("point")
p <- p %>% remove_geom("Line")
p <- p %>% + geom_line(aes(x = Pseudotime, y = expectation), size=1)
show(p)

2.3.2 Genes in pseudotime with branches (Selected genes)

p <- plot_genes_branched_pseudotime(monocle[genes_of_interest,], color_by="cluster") + scale_color_manual(values=colours)
show(p)

p <- p %>% remove_geom("point")
show(p)

3 Seurat tSNE plots

p <- cytokit::tsne(seurat, label=FALSE)
show(p)

p <- tsne_plot_clusters_highlighted(seurat, selected_clusters, legend=TRUE)
show(p)

p <- p + theme(legend.position = "none")
show(p)

p <- tsne_plot_clusters_highlighted_with_pseudotime(seurat, monocle, selected_clusters, legend=TRUE)
show(p)

p <- p + theme(legend.position = "none")
show(p)

4 Save monocle object to directory, and write pseudotime of cells to table.

save(monocle, file=file.path(monocle_objects_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11.Rda"))
cells_pseudotime <- pData(monocle) %>% select(cell, Pseudotime) %>% rename(pseudotime=Pseudotime)
write.table(cells_pseudotime, file.path(tables_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11_cell_pseudotime.txt"), sep="\t", quote=FALSE, row.names=FALSE)

5 Session info

sessionInfo()
## R version 3.5.0 (2018-04-23)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
## 
## Matrix products: default
## BLAS/LAPACK: /var/chroots/hydraex-centos-7/usr/lib64/R/lib/libRblas.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
##  [1] splines   stats4    parallel  stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] viridis_0.5.1       viridisLite_0.3.0   forcats_0.4.0      
##  [4] stringr_1.4.0       dplyr_0.8.0.1       purrr_0.3.0        
##  [7] tidyr_0.8.2         tibble_2.0.1        tidyverse_1.2.1    
## [10] Seurat_2.3.4        cowplot_0.9.4       R.utils_2.8.0      
## [13] R.oo_1.22.0         R.methodsS3_1.7.1   readr_1.3.1        
## [16] readxl_1.3.0        patchwork_0.0.1     monocle_2.10.1     
## [19] DDRTree_0.1.5       irlba_2.3.3         VGAM_1.1-1         
## [22] Biobase_2.42.0      BiocGenerics_0.28.0 Matrix_1.2-15      
## [25] kableExtra_1.0.1    ggedit_0.3.0        ggplot2_3.1.0      
## [28] cytokit_0.6.0       pheatmap_1.0.12     colorRamps_2.3     
## 
## loaded via a namespace (and not attached):
##   [1] snow_0.4-3           backports_1.1.3      Hmisc_4.2-0         
##   [4] plyr_1.8.4           igraph_1.2.4         lazyeval_0.2.2      
##   [7] densityClust_0.3     fastICA_1.2-1        digest_0.6.18       
##  [10] foreach_1.4.4        htmltools_0.3.6      lars_1.2            
##  [13] gdata_2.18.0         magrittr_1.5         checkmate_1.9.1     
##  [16] cluster_2.0.7-1      mixtools_1.1.0       ROCR_1.0-7          
##  [19] limma_3.38.3         modelr_0.1.3         matrixStats_0.54.0  
##  [22] docopt_0.6.1         colorspace_1.4-0     ggrepel_0.8.0       
##  [25] rvest_0.3.2          haven_2.0.0          xfun_0.4            
##  [28] sparsesvd_0.1-4      crayon_1.3.4         jsonlite_1.6        
##  [31] survival_2.43-3      zoo_1.8-4            iterators_1.0.10    
##  [34] ape_5.2              glue_1.3.0           gtable_0.2.0        
##  [37] webshot_0.5.1        kernlab_0.9-27       prabclus_2.2-7      
##  [40] DEoptimR_1.0-8       scales_1.0.0         mvtnorm_1.0-8       
##  [43] bibtex_0.4.2         miniUI_0.1.1.1       Rcpp_1.0.0          
##  [46] metap_1.1            dtw_1.20-1           xtable_1.8-3        
##  [49] htmlTable_1.13.1     reticulate_1.11.1    foreign_0.8-71      
##  [52] bit_1.1-14           proxy_0.4-22         mclust_5.4.2        
##  [55] SDMTools_1.1-221     Formula_1.2-3        tsne_0.1-3          
##  [58] htmlwidgets_1.3      httr_1.4.0           FNN_1.1.3           
##  [61] gplots_3.0.1.1       RColorBrewer_1.1-2   shinyAce_0.3.3      
##  [64] fpc_2.1-11.1         acepack_1.4.1        modeltools_0.2-22   
##  [67] ica_1.0-2            pkgconfig_2.0.2      flexmix_2.3-14      
##  [70] nnet_7.3-12          labeling_0.3         tidyselect_0.2.5    
##  [73] rlang_0.3.1          reshape2_1.4.3       later_0.8.0         
##  [76] cellranger_1.1.0     munsell_0.5.0        tools_3.5.0         
##  [79] cli_1.0.1            generics_0.0.2       broom_0.5.1         
##  [82] ggridges_0.5.1       evaluate_0.13        shinyBS_0.61        
##  [85] yaml_2.2.0           npsurv_0.4-0         knitr_1.21          
##  [88] bit64_0.9-7          fitdistrplus_1.0-14  robustbase_0.93-3   
##  [91] caTools_1.17.1.1     randomForest_4.6-14  RANN_2.6.1          
##  [94] pbapply_1.4-0        nlme_3.1-137         mime_0.6            
##  [97] slam_0.1-44          xml2_1.2.0           hdf5r_1.0.0         
## [100] compiler_3.5.0       rstudioapi_0.9.0     png_0.1-7           
## [103] lsei_1.2-0           stringi_1.3.1        highr_0.7           
## [106] lattice_0.20-35      trimcluster_0.1-2.1  HSMMSingleCell_1.2.0
## [109] pillar_1.3.1         combinat_0.0-8       Rdpack_0.10-1       
## [112] lmtest_0.9-36        data.table_1.12.0    bitops_1.0-6        
## [115] gbRd_0.4-11          httpuv_1.5.1         R6_2.4.0            
## [118] latticeExtra_0.6-28  promises_1.0.1       KernSmooth_2.23-15  
## [121] gridExtra_2.3        codetools_0.2-15     MASS_7.3-51.1       
## [124] gtools_3.8.1         assertthat_0.2.0     withr_2.1.2         
## [127] qlcMatrix_0.9.7      diptest_0.75-7       doSNOW_1.0.16       
## [130] hms_0.4.2            grid_3.5.0           rpart_4.1-13        
## [133] class_7.3-14         rmarkdown_1.11       segmented_0.5-3.0   
## [136] Rtsne_0.15           lubridate_1.7.4      shiny_1.2.0         
## [139] base64enc_0.1-3